The dpkg warnings are real since your system is a little out of sync when you reflash it. This is because some package information is lost, which is why it says that file lists such libctf0:arm64 are missing. The good news is that your ZED Link driver installs correctly and the symlinks and services are set up, so everything should still work.
To repair the package database and get rid of the warnings, do the following:
sudo apt --fix-broken install
sudo dpkg --configure -a
sudo apt-get update
sudo apt-get upgrade
This will fix any missing information and set up any packages that are only partly installed. Then, run again:
dpkg -l | grep ^..r
to look for packages that are still broken. If any do show up, running sudo apt-get install --reinstall typically gets rid of them.
In brief, the warnings are common after a reflash and don’t signify that your ZED Box driver is defective. Cleaning the dpkg/apt database will get rid of the noise and make the system more stable.